Skip to main content
Glama
Sign In
gromacs-mcp

gromacs-mcp

by Alierkn
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

genion

Add counter-ions to a molecular system by replacing solvent molecules, neutralizing charge or achieving a specified ion concentration.

Instructions

Add counter-ions by replacing solvent molecules.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "tpr": "<tpr>",
      "topology": "<topology>",
      "workdir": "<workdir>"
    },
    "name": "genion"
  }
}

Input Schema

NameRequiredDescriptionDefault
tprYes
groupNoSOL
nnameNoCL
pnameNoNA
outputNoions.gro
neutralNo
workdirYes
topologyYes
extra_argsNo
concentrationNo

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

C2.4/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description mentions 'replace solvent molecules' implying modification, but does not disclose behavioral traits such as whether it requires specific permissions, what files are changed, or side effects. Annotations indicate it is not read-only and not destructive, but description adds minimal context beyond that.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise (one sentence), but it is too short to convey necessary information. While concise, it sacrifices completeness and clarity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the high parameter count (10), lack of schema descriptions, and absence of output schema details, the description is woefully incomplete. It does not cover parameters, return values, or usage context adequately.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 10 parameters and 0% schema description coverage, the description fails to explain any parameter meanings. It only hints at 'solvent' which relates to the 'group' default, but does not clarify the function of parameters like pname, nname, concentration, etc.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states that the tool adds counter-ions by replacing solvent molecules, which is a specific verb and resource. However, it does not differentiate from sibling tools like solvate or pdb2gmx that also modify the system.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives, nor any prerequisites or context for usage. It simply states the action without any when-to-use or when-not-to-use information.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Deploy Server

Other Tools